Jirí Sponer
Orcid: 0000-0001-6558-6186
According to our database1,
Jirí Sponer
authored at least 14 papers
between 1995 and 2023.
Collaborative distances:
Collaborative distances:
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Bibliography
2023
Complexity of Guanine Quadruplex Unfolding Pathways Revealed by Atomistic Pulling Simulations.
J. Chem. Inf. Model., August, 2023
Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations.
J. Chem. Inf. Model., May, 2023
Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes.
J. Chem. Inf. Model., April, 2023
2022
Multiscale Modeling of Phosphate···π Contacts in RNA U-Turns Exposes Differences between Quantum-Chemical and AMBER Force Field Descriptions.
J. Chem. Inf. Model., 2022
A Computational Quantum-Based Perspective on the Molecular Origins of Life's Building Blocks.
Entropy, 2022
2021
Short-Range Imbalances in the AMBER Lennard-Jones Potential for (Deoxy)Ribose···Nucleobase Lone-Pair···π Contacts in Nucleic Acids.
J. Chem. Inf. Model., 2021
2019
Comment on "Evaluating Unexpectedly Short Non-covalent Distances in X-ray Crystal Structures of Proteins with Electronic Structure Analysis".
J. Chem. Inf. Model., 2019
2018
Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study.
PLoS Comput. Biol., 2018
2017
Influence of BII Backbone Substates on DNA Twist: A Unified View and Comparison of Simulation and Experiment for All 136 Distinct Tetranucleotide Sequences.
J. Chem. Inf. Model., 2017
2013
Entropy, 2013
2009
Interactions of the "piano-stool" [ruthenium(II) (eta<sup>6</sup>-arene)(en)CL]<sup>+</sup> complexes with water and nucleobases; ab initio and DFT study.
J. Comput. Chem., 2009
1997
Performance of empirical potentials (AMBER, CFF95, CVFF, CHARMM, OPLS, POLTEV), semiempirical quantum chemical methods (AM1, MNDO/M, PM3), and ab initio Hartree-Fock method for interaction of DNA bases: Comparison with nonempirical beyond Hartree-Fock results.
J. Comput. Chem., 1997
1996
Base stacking in cytosine dimer. A comparison of correlated ab initio calculations with three empirical potential models and density functional theory calculations.
J. Comput. Chem., 1996
1995